CD-HIT reduction 99%

30%, 4 clusters

graphpart needle --fasta-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Sequences/Datasets_for_graph-part_cdhit_0.99.fa --threshold 0.3 --out-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Graph-part_results/graphpart_res_cdhit0.99_4.csv --labels-name label --partitions 4 --threads 24 --save-checkpoint-path graph-part_edgelist_99.csv

30%, 5 clusters

graphpart precomputed --fasta-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Sequences/Datasets_for_graph-part_cdhit_0.99.fa --threshold 0.3 --out-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Graph-part_results/graphpart_res_cdhit0.99_5.csv --labels-name label --partitions 5 --edge-file graph-part_edgelist_99.csv

30%, 6 clusters

graphpart precomputed --fasta-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Sequences/Datasets_for_graph-part_cdhit_0.99.fa --threshold 0.3 --out-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Graph-part_results/graphpart_res_cdhit0.99_6.csv --labels-name label --partitions 6 --edge-file graph-part_edgelist_99.csv

40%, 4 clusters

graphpart precomputed --fasta-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Sequences/Datasets_for_graph-part_cdhit_0.99.fa --threshold 0.4 --out-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Graph-part_results/graphpart_res_cdhit0.99_4_thresh0.4.csv --labels-name label --partitions 4 --edge-file graph-part_edgelist_99.csv

40%, 5 clusters

graphpart precomputed --fasta-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Sequences/Datasets_for_graph-part_cdhit_0.99.fa --threshold 0.4 --out-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Graph-part_results/graphpart_res_cdhit0.99_5_thresh0.4.csv --labels-name label --partitions 5 --edge-file graph-part_edgelist_99.csv

40%, 6 clusters

graphpart precomputed --fasta-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Sequences/Datasets_for_graph-part_cdhit_0.99.fa --threshold 0.4 --out-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Graph-part_results/graphpart_res_cdhit0.99_6_thresh0.4.csv --labels-name label --partitions 6 --edge-file graph-part_edgelist_99.csv

50%, 4 clusters

graphpart precomputed --fasta-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Sequences/Datasets_for_graph-part_cdhit_0.99.fa --threshold 0.5 --out-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Graph-part_results/graphpart_res_cdhit0.99_4_thresh0.5.csv --labels-name label --partitions 4 --edge-file graph-part_edgelist_99.csv

50%, 5 clusters

graphpart precomputed --fasta-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Sequences/Datasets_for_graph-part_cdhit_0.99.fa --threshold 0.5 --out-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Graph-part_results/graphpart_res_cdhit0.99_5_thresh0.5.csv --labels-name label --partitions 5 --edge-file graph-part_edgelist_99.csv

50%, 6 clusters

graphpart precomputed --fasta-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Sequences/Datasets_for_graph-part_cdhit_0.99.fa --threshold 0.5 --out-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Graph-part_results/graphpart_res_cdhit0.99_6_thresh0.5.csv --labels-name label --partitions 6 --edge-file graph-part_edgelist_99.csv

30%, 4 clusters, no moving

graphpart precomputed --fasta-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Sequences/Datasets_for_graph-part_cdhit_0.99.fa --threshold 0.3 --out-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Graph-part_results/graphpart_res_cdhit0.99_4_nomoving.csv --labels-name label --partitions 4 --edge-file graph-part_edgelist_99.csv --no-moving

30%, 5 clusters, no moving

graphpart precomputed --fasta-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Sequences/Datasets_for_graph-part_cdhit_0.99.fa --threshold 0.3 --out-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Graph-part_results/graphpart_res_cdhit0.99_5_nomoving.csv --labels-name label --partitions 5 --edge-file graph-part_edgelist_99.csv --no-moving

30%, 6 clusters, no moving

graphpart precomputed --fasta-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Sequences/Datasets_for_graph-part_cdhit_0.99.fa --threshold 0.3 --out-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Graph-part_results/graphpart_res_cdhit0.99_6_nomoving.csv --labels-name label --partitions 6 --edge-file graph-part_edgelist_99.csv --no-moving

40%, 4 clusters, no moving

graphpart precomputed --fasta-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Sequences/Datasets_for_graph-part_cdhit_0.99.fa --threshold 0.4 --out-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Graph-part_results/graphpart_res_cdhit0.99_4_thresh0.4_nomoving.csv --labels-name label --partitions 4 --edge-file graph-part_edgelist_99.csv --no-moving

40%, 5 clusters, no moving

graphpart precomputed --fasta-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Sequences/Datasets_for_graph-part_cdhit_0.99.fa --threshold 0.4 --out-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Graph-part_results/graphpart_res_cdhit0.99_5_thresh0.4_nomoving.csv --labels-name label --partitions 5 --edge-file graph-part_edgelist_99.csv --no-moving

40%, 6 clusters, no moving

graphpart precomputed --fasta-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Sequences/Datasets_for_graph-part_cdhit_0.99.fa --threshold 0.4 --out-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Graph-part_results/graphpart_res_cdhit0.99_6_thresh0.4_nomoving.csv --labels-name label --partitions 6 --edge-file graph-part_edgelist_99.csv --no-moving

50%, 4 clusters, no moving

graphpart precomputed --fasta-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Sequences/Datasets_for_graph-part_cdhit_0.99.fa --threshold 0.5 --out-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Graph-part_results/graphpart_res_cdhit0.99_4_thresh0.5_nomoving.csv --labels-name label --partitions 4 --edge-file graph-part_edgelist_99.csv --no-moving

50%, 5 clusters, no moving

graphpart precomputed --fasta-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Sequences/Datasets_for_graph-part_cdhit_0.99.fa --threshold 0.5 --out-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Graph-part_results/graphpart_res_cdhit0.99_5_thresh0.5_nomoving.csv --labels-name label --partitions 5 --edge-file graph-part_edgelist_99.csv --no-moving

50%, 6 clusters, no moving

graphpart precomputed --fasta-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Sequences/Datasets_for_graph-part_cdhit_0.99.fa --threshold 0.5 --out-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Graph-part_results/graphpart_res_cdhit0.99_6_thresh0.5_nomoving.csv --labels-name label --partitions 6 --edge-file graph-part_edgelist_99.csv --no-moving

CD-HIT 95%

30%, 4 clusters

graphpart needle --fasta-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Sequences/Datasets_for_graph-part_cdhit_0.95.fa --threshold 0.3 --out-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Graph-part_results/graphpart_res_cdhit0.95_4.csv --labels-name label --partitions 4 --threads 24 --save-checkpoint-path graph-part_edgelist_95.csv

30%, 5 clusters

graphpart precomputed --fasta-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Sequences/Datasets_for_graph-part_cdhit_0.95.fa --threshold 0.3 --out-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Graph-part_results/graphpart_res_cdhit0.95_5.csv --labels-name label --partitions 5 --edge-file graph-part_edgelist_95.csv

30%, 6 clusters

graphpart precomputed --fasta-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Sequences/Datasets_for_graph-part_cdhit_0.95.fa --threshold 0.3 --out-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Graph-part_results/graphpart_res_cdhit0.95_6.csv --labels-name label --partitions 6 --edge-file graph-part_edgelist_95.csv

40%, 4 clusters

graphpart precomputed --fasta-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Sequences/Datasets_for_graph-part_cdhit_0.95.fa --threshold 0.4 --out-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Graph-part_results/graphpart_res_cdhit0.95_4_thresh0.4.csv --labels-name label --partitions 4 --edge-file graph-part_edgelist_95.csv

40%, 5 clusters

graphpart precomputed --fasta-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Sequences/Datasets_for_graph-part_cdhit_0.95.fa --threshold 0.4 --out-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Graph-part_results/graphpart_res_cdhit0.95_5_thresh0.4.csv --labels-name label --partitions 5 --edge-file graph-part_edgelist_95.csv

40%, 6 clusters

graphpart precomputed --fasta-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Sequences/Datasets_for_graph-part_cdhit_0.95.fa --threshold 0.4 --out-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Graph-part_results/graphpart_res_cdhit0.95_6_thresh0.4.csv --labels-name label --partitions 6 --edge-file graph-part_edgelist_95.csv

50%, 4 clusters

graphpart precomputed --fasta-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Sequences/Datasets_for_graph-part_cdhit_0.95.fa --threshold 0.5 --out-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Graph-part_results/graphpart_res_cdhit0.95_4_thresh0.5.csv --labels-name label --partitions 4 --edge-file graph-part_edgelist_95.csv

50%, 5 clusters

graphpart precomputed --fasta-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Sequences/Datasets_for_graph-part_cdhit_0.95.fa --threshold 0.5 --out-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Graph-part_results/graphpart_res_cdhit0.95_5_thresh0.5.csv --labels-name label --partitions 5 --edge-file graph-part_edgelist_95.csv

50%, 6 clusters

graphpart precomputed --fasta-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Sequences/Datasets_for_graph-part_cdhit_0.95.fa --threshold 0.5 --out-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Graph-part_results/graphpart_res_cdhit0.95_6_thresh0.5.csv --labels-name label --partitions 6 --edge-file graph-part_edgelist_95.csv

30%, 4 clusters, no moving

graphpart precomputed --fasta-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Sequences/Datasets_for_graph-part_cdhit_0.95.fa --threshold 0.3 --out-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Graph-part_results/graphpart_res_cdhit0.95_4_nomoving.csv --labels-name label --partitions 4 --edge-file graph-part_edgelist_95.csv --no-moving

30%, 5 clusters, no moving

graphpart precomputed --fasta-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Sequences/Datasets_for_graph-part_cdhit_0.95.fa --threshold 0.3 --out-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Graph-part_results/graphpart_res_cdhit0.95_5_nomoving.csv --labels-name label --partitions 5 --edge-file graph-part_edgelist_95.csv --no-moving

30%, 6 clusters, no moving

graphpart precomputed --fasta-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Sequences/Datasets_for_graph-part_cdhit_0.95.fa --threshold 0.3 --out-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Graph-part_results/graphpart_res_cdhit0.95_6_nomoving.csv --labels-name label --partitions 6 --edge-file graph-part_edgelist_95.csv --no-moving

40%, 4 clusters, no moving

graphpart precomputed --fasta-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Sequences/Datasets_for_graph-part_cdhit_0.95.fa --threshold 0.4 --out-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Graph-part_results/graphpart_res_cdhit0.95_4_thresh0.4_nomoving.csv --labels-name label --partitions 4 --edge-file graph-part_edgelist_95.csv --no-moving

40%, 5 clusters, no moving

graphpart precomputed --fasta-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Sequences/Datasets_for_graph-part_cdhit_0.95.fa --threshold 0.4 --out-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Graph-part_results/graphpart_res_cdhit0.95_5_thresh0.4_nomoving.csv --labels-name label --partitions 5 --edge-file graph-part_edgelist_95.csv --no-moving

40%, 6 clusters, no moving

graphpart precomputed --fasta-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Sequences/Datasets_for_graph-part_cdhit_0.95.fa --threshold 0.4 --out-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Graph-part_results/graphpart_res_cdhit0.95_6_thresh0.4_nomoving.csv --labels-name label --partitions 6 --edge-file graph-part_edgelist_95.csv --no-moving

50%, 4 clusters, no moving

graphpart precomputed --fasta-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Sequences/Datasets_for_graph-part_cdhit_0.95.fa --threshold 0.5 --out-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Graph-part_results/graphpart_res_cdhit0.95_4_thresh0.5_nomoving.csv --labels-name label --partitions 4 --edge-file graph-part_edgelist_95.csv --no-moving

50%, 5 clusters, no moving

graphpart precomputed --fasta-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Sequences/Datasets_for_graph-part_cdhit_0.95.fa --threshold 0.5 --out-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Graph-part_results/graphpart_res_cdhit0.95_5_thresh0.5_nomoving.csv --labels-name label --partitions 5 --edge-file graph-part_edgelist_95.csv --no-moving

50%, 6 clusters, no moving

graphpart precomputed --fasta-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Sequences/Datasets_for_graph-part_cdhit_0.95.fa --threshold 0.5 --out-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Graph-part_results/graphpart_res_cdhit0.95_6_thresh0.5_nomoving.csv --labels-name label --partitions 6 --edge-file graph-part_edgelist_95.csv --no-moving

Simple initialization

30%, 4 clusters, no moving, simple initialization

graphpart needle --fasta-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Sequences/Datasets_for_graph-part.fa --threshold 0.3 --out-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Graph-part_results/graphpart_res_4_nomoving_simple.csv --no-moving --labels-name label --partitions 4 --threads 24 --initialization-mode simple

40%, 4 clusters, no moving, simple initialization

graphpart needle --fasta-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Sequences/Datasets_for_graph-part.fa --threshold 0.4 --out-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Graph-part_results/graphpart_res_4_nomoving_thresh0.4_simple.csv --no-moving --labels-name label --partitions 4 --threads 24 --initialization-mode simple

50%, 4 clusters, no moving, simple initialization

graphpart needle --fasta-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Sequences/Datasets_for_graph-part.fa --threshold 0.5 --out-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Graph-part_results/graphpart_res_4_nomoving_thresh0.5_simple.csv --no-moving --labels-name label --partitions 4 --threads 24 --initialization-mode simple

30%, 5 clusters, no moving, simple initialization

graphpart needle --fasta-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Sequences/Datasets_for_graph-part.fa --threshold 0.3 --out-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Graph-part_results/graphpart_res_5_nomoving_simple.csv --no-moving --labels-name label --partitions 5 --threads 24 --initialization-mode simple

40%, 5 clusters, no moving, simple initialization

graphpart needle --fasta-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Sequences/Datasets_for_graph-part.fa --threshold 0.4 --out-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Graph-part_results/graphpart_res_5_nomoving_thresh0.4_simple.csv --no-moving --labels-name label --partitions 5 --threads 24 --initialization-mode simple

50%, 5 clusters, no moving, simple initialization

graphpart needle --fasta-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Sequences/Datasets_for_graph-part.fa --threshold 0.5 --out-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Graph-part_results/graphpart_res_5_nomoving_thresh0.5_simple.csv --no-moving --labels-name label --partitions 5 --threads 24 --initialization-mode simple

30%, 4 clusters, moving, simple initialization

graphpart needle --fasta-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Sequences/Datasets_for_graph-part.fa --threshold 0.3 --out-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Graph-part_results/graphpart_res_4_simple.csv --labels-name label --partitions 4 --threads 24 --initialization-mode simple

40%, 4 clusters, moving, simple initialization

graphpart needle --fasta-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Sequences/Datasets_for_graph-part.fa --threshold 0.4 --out-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Graph-part_results/graphpart_res_4_thresh0.4_simple.csv --labels-name label --partitions 4 --threads 24 --initialization-mode simple

50%, 4 clusters, moving, simple initialization

graphpart needle --fasta-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Sequences/Datasets_for_graph-part.fa --threshold 0.5 --out-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Graph-part_results/graphpart_res_4_thresh0.5_simple.csv --labels-name label --partitions 4 --threads 24 --initialization-mode simple

30%, 5 clusters, moving, simple initialization

graphpart needle --fasta-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Sequences/Datasets_for_graph-part.fa --threshold 0.3 --out-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Graph-part_results/graphpart_res_5_simple.csv --labels-name label --partitions 5 --threads 24 --initialization-mode simple

40%, 5 clusters, moving, simple initialization

graphpart needle --fasta-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Sequences/Datasets_for_graph-part.fa --threshold 0.4 --out-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Graph-part_results/graphpart_res_5_thresh0.4_simple.csv --labels-name label --partitions 5 --threads 24 --initialization-mode simple

50%, 5 clusters, moving, simple initialization

graphpart needle --fasta-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Sequences/Datasets_for_graph-part.fa --threshold 0.5 --out-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Graph-part_results/graphpart_res_5_thresh0.5_simple.csv --labels-name label --partitions 5 --threads 24 --initialization-mode simple

CD-HIT reduction 90%

30%, 4 clusters

graphpart needle --fasta-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Sequences/Datasets_for_graph-part_cdhit_0.90.fa --threshold 0.3 --out-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Graph-part_results/graphpart_res_cdhit0.90_4.csv --labels-name label --partitions 4 --threads 24 --save-checkpoint-path graph-part_edgelist_90.csv

30%, 5 clusters

graphpart precomputed --fasta-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Sequences/Datasets_for_graph-part_cdhit_0.90.fa --threshold 0.3 --out-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Graph-part_results/graphpart_res_cdhit0.90_5.csv --labels-name label --partitions 5 --edge-file graph-part_edgelist_90.csv

30%, 6 clusters

graphpart precomputed --fasta-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Sequences/Datasets_for_graph-part_cdhit_0.90.fa --threshold 0.3 --out-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Graph-part_results/graphpart_res_cdhit0.90_6.csv --labels-name label --partitions 6 --edge-file graph-part_edgelist_90.csv

40%, 4 clusters

graphpart precomputed --fasta-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Sequences/Datasets_for_graph-part_cdhit_0.90.fa --threshold 0.4 --out-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Graph-part_results/graphpart_res_cdhit0.90_4_thresh0.4.csv --labels-name label --partitions 4 --edge-file graph-part_edgelist_90.csv

40%, 5 clusters

graphpart precomputed --fasta-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Sequences/Datasets_for_graph-part_cdhit_0.90.fa --threshold 0.4 --out-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Graph-part_results/graphpart_res_cdhit0.90_5_thresh0.4.csv --labels-name label --partitions 5 --edge-file graph-part_edgelist_90.csv

40%, 6 clusters

graphpart precomputed --fasta-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Sequences/Datasets_for_graph-part_cdhit_0.90.fa --threshold 0.4 --out-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Graph-part_results/graphpart_res_cdhit0.90_6_thresh0.4.csv --labels-name label --partitions 6 --edge-file graph-part_edgelist_90.csv

50%, 4 clusters

graphpart precomputed --fasta-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Sequences/Datasets_for_graph-part_cdhit_0.90.fa --threshold 0.5 --out-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Graph-part_results/graphpart_res_cdhit0.90_4_thresh0.5.csv --labels-name label --partitions 4 --edge-file graph-part_edgelist_90.csv

50%, 5 clusters

graphpart precomputed --fasta-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Sequences/Datasets_for_graph-part_cdhit_0.90.fa --threshold 0.5 --out-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Graph-part_results/graphpart_res_cdhit0.90_5_thresh0.5.csv --labels-name label --partitions 5 --edge-file graph-part_edgelist_90.csv

50%, 6 clusters

graphpart precomputed --fasta-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Sequences/Datasets_for_graph-part_cdhit_0.90.fa --threshold 0.5 --out-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Graph-part_results/graphpart_res_cdhit0.90_6_thresh0.5.csv --labels-name label --partitions 6 --edge-file graph-part_edgelist_90.csv

30%, 4 clusters, no moving

graphpart precomputed --fasta-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Sequences/Datasets_for_graph-part_cdhit_0.90.fa --threshold 0.3 --out-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Graph-part_results/graphpart_res_cdhit0.90_4_nomoving.csv --labels-name label --partitions 4 --edge-file graph-part_edgelist_90.csv --no-moving

30%, 5 clusters, no moving

graphpart precomputed --fasta-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Sequences/Datasets_for_graph-part_cdhit_0.90.fa --threshold 0.3 --out-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Graph-part_results/graphpart_res_cdhit0.90_5_nomoving.csv --labels-name label --partitions 5 --edge-file graph-part_edgelist_90.csv --no-moving

30%, 6 clusters, no moving

graphpart precomputed --fasta-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Sequences/Datasets_for_graph-part_cdhit_0.90.fa --threshold 0.3 --out-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Graph-part_results/graphpart_res_cdhit0.90_6_nomoving.csv --labels-name label --partitions 6 --edge-file graph-part_edgelist_90.csv --no-moving

40%, 4 clusters, no moving

graphpart precomputed --fasta-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Sequences/Datasets_for_graph-part_cdhit_0.90.fa --threshold 0.4 --out-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Graph-part_results/graphpart_res_cdhit0.90_4_thresh0.4_nomoving.csv --labels-name label --partitions 4 --edge-file graph-part_edgelist_90.csv --no-moving

40%, 5 clusters, no moving

graphpart precomputed --fasta-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Sequences/Datasets_for_graph-part_cdhit_0.90.fa --threshold 0.4 --out-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Graph-part_results/graphpart_res_cdhit0.90_5_thresh0.4_nomoving.csv --labels-name label --partitions 5 --edge-file graph-part_edgelist_90.csv --no-moving

40%, 6 clusters, no moving

graphpart precomputed --fasta-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Sequences/Datasets_for_graph-part_cdhit_0.90.fa --threshold 0.4 --out-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Graph-part_results/graphpart_res_cdhit0.90_6_thresh0.4_nomoving.csv --labels-name label --partitions 6 --edge-file graph-part_edgelist_90.csv --no-moving

50%, 4 clusters, no moving

graphpart precomputed --fasta-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Sequences/Datasets_for_graph-part_cdhit_0.90.fa --threshold 0.5 --out-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Graph-part_results/graphpart_res_cdhit0.90_4_thresh0.5_nomoving.csv --labels-name label --partitions 4 --edge-file graph-part_edgelist_90.csv --no-moving

50%, 5 clusters, no moving

graphpart precomputed --fasta-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Sequences/Datasets_for_graph-part_cdhit_0.90.fa --threshold 0.5 --out-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Graph-part_results/graphpart_res_cdhit0.90_5_thresh0.5_nomoving.csv --labels-name label --partitions 5 --edge-file graph-part_edgelist_90.csv --no-moving

50%, 6 clusters, no moving

graphpart precomputed --fasta-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Sequences/Datasets_for_graph-part_cdhit_0.90.fa --threshold 0.5 --out-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Graph-part_results/graphpart_res_cdhit0.90_6_thresh0.5_nomoving.csv --labels-name label --partitions 6 --edge-file graph-part_edgelist_90.csv --no-moving

No moving option

30%, 4 clusters

graphpart needle --fasta-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Sequences/Datasets_for_graph-part.fa --threshold 0.3 --out-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Graph-part_results/graphpart_res_40_nomoving.csv --no-moving --labels-name label --partitions 4 --threads 24

40%, 4 clusters

graphpart needle --fasta-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Sequences/Datasets_for_graph-part.fa --threshold 0.4 --out-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Graph-part_results/graphpart_res_4_nomoving_thresh0.4.csv --no-moving --labels-name label --partitions 4 --threads 24

50%, 4 clusters

graphpart needle --fasta-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Sequences/Datasets_for_graph-part.fa --threshold 0.5 --out-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Graph-part_results/graphpart_res_4_nomoving_thresh0.5.csv --no-moving --labels-name label --partitions 4 --threads 24

60%, 4 clusters

graphpart needle --fasta-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Sequences/Datasets_for_graph-part.fa --threshold 0.6 --out-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Graph-part_results/graphpart_res_4_nomoving_thresh0.6.csv --no-moving --labels-name label --partitions 4 --threads 24

40%, 5 clusters

graphpart needle --fasta-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Sequences/Datasets_for_graph-part.fa --threshold 0.4 --out-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Graph-part_results/graphpart_res_5_nomoving_thresh0.4.csv --no-moving --labels-name label --partitions 5 --threads 24

50%, 5 clusters

graphpart needle --fasta-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Sequences/Datasets_for_graph-part.fa --threshold 0.5 --out-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Graph-part_results/graphpart_res_5_nomoving_thresh0.5.csv --no-moving --labels-name label --partitions 5 --threads 24

60%, 5 clusters

graphpart needle --fasta-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Sequences/Datasets_for_graph-part.fa --threshold 0.6 --out-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Graph-part_results/graphpart_res_5_nomoving_thresh0.6.csv --no-moving --labels-name label --partitions 5 --threads 24

30%, 6 clusters

graphpart needle --fasta-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Sequences/Datasets_for_graph-part.fa --threshold 0.3 --out-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Graph-part_results/graphpart_res_6_nomoving.csv --no-moving --labels-name label --partitions 6 --threads 24

40%, 6 clusters

graphpart needle --fasta-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Sequences/Datasets_for_graph-part.fa --threshold 0.4 --out-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Graph-part_results/graphpart_res_6_nomoving_thresh0.4.csv --no-moving --labels-name label --partitions 6 --threads 24

50%, 6 clusters

graphpart needle --fasta-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Sequences/Datasets_for_graph-part.fa --threshold 0.5 --out-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Graph-part_results/graphpart_res_6_nomoving_thresh0.5.csv --no-moving --labels-name label --partitions 6 --threads 24

Partitioning within classes

30%, 6 clusters

30%, 6 clusters, no moving

30%, 4 clusters

30%, 4 clusters, no moving

40%, 4 clusters, no moving

50%, 4 clusters, no moving

40%, 5 clusters, no moving

50%, 5 clusters, no moving

40%, 6 clusters, no moving

50%, 6 clusters, no moving

Threshold = 30%

Needle, 11 clusters

graphpart needle --fasta-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Sequences/Datasets_for_graph-part.fa --threshold 0.3 --out-file graphpart_res_11.csv --labels-name label --partitions 11 --threads 20

Needle, 6 clusters

graphpart needle --fasta-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Sequences/Datasets_for_graph-part.fa --threshold 0.3 --out-file graphpart_res_6.csv --labels-name label --partitions 6 --threads 20

Needle, 4 clusters

graphpart needle --fasta-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Sequences/Datasets_for_graph-part.fa --threshold 0.3 --out-file graphpart_res_4.csv --labels-name label --partitions 4 --threads 20

mmseqs2, 11 clusters

graphpart mmseqs2 --fasta-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Sequences/Datasets_for_graph-part.fa --threshold 0.3 --out-file graphpart_res_11_mmseqs.csv --labels-name label --partitions 11

mmseqs2, 6 clusters

graphpart mmseqs2 --fasta-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Sequences/Datasets_for_graph-part.fa --threshold 0.3 --out-file graphpart_res_6_mmseqs.csv --labels-name label --partitions 6

mmseqs2, 4 clusters

graphpart mmseqs2 --fasta-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Sequences/Datasets_for_graph-part.fa --threshold 0.3 --out-file graphpart_res_4_mmseqs.csv --labels-name label --partitions 4

Threshold = 40%

Needle, 11 clusters

graphpart needle --fasta-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Sequences/Datasets_for_graph-part.fa --threshold 0.4 --out-file graphpart_res_11_thresh0.4.csv --labels-name label --partitions 11 --threads 20

Needle, 6 clusters

graphpart needle --fasta-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Sequences/Datasets_for_graph-part.fa --threshold 0.4 --out-file graphpart_res_6_thresh0.4.csv --labels-name label --partitions 6 --threads 20

Needle, 4 clusters

graphpart needle --fasta-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Sequences/Datasets_for_graph-part.fa --threshold 0.4 --out-file graphpart_res_4_thresh0.4.csv --labels-name label --partitions 4 --threads 20

mmseqs2, 11 clusters

graphpart mmseqs2 --fasta-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Sequences/Datasets_for_graph-part.fa --threshold 0.4 --out-file graphpart_res_11_mmseqs_thresh0.4.csv --labels-name label --partitions 11

mmseqs2, 6 clusters

graphpart mmseqs2 --fasta-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Sequences/Datasets_for_graph-part.fa --threshold 0.4 --out-file graphpart_res_6_mmseqs_thresh0.4.csv --labels-name label --partitions 6

mmseqs2, 4 clusters

graphpart mmseqs2 --fasta-file ~/Dropbox/Projekty/BioNgramProjects/PlastoGram/Sequences/Datasets_for_graph-part.fa --threshold 0.4 --out-file graphpart_res_4_mmseqs_thresh0.4.csv --labels-name label --partitions 4